You are here

All Tutorials

MatlabMPI is a Matlab implementation of the Message Passing Interface (MPI) standard made by Lincoln Laboratory at MIT. It allows any Matlab program to exploit multiple processors. MatlabMPI currently implements the basic functions that are the core of the point-to-point communications standard.

This tutorial focuses on the use of MatlabMPI as a tool of parallel computing in the Matlab environment. A one-hour, hands-on session will follow the lecture to help users become familiar with the concepts/syntax and develop simple application codes.

The Supercomputing Institute maintains a wide range of software packages dedicated to structural biology. This tutorial offers an overview of those packages, focusing on how to start using them. In particular, we will look at Auremol, CCP4, CNS/Xplor, NMRPipe, etc.

Schrödinger, LLC provides a wide range of computational chemistry and molecule modeling software used to build, display, manipulate, simulate, and calculate molecular properties. The common interface, Maestro, is the graphic user interface that acts as a front end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro, in addition to demonstrating its interface to some of its molecular modeling and computational chemistry modules.

Building a web interface for your database will expand the use of the database. A web-based database is more convenient for viewing and sharing data, especially in the field of bioinformatics. This tutorial will introduce you to building a web database using CGI/PERL and PHP in the Unix environment. We will cover the dynamic web page development using CGI or PHP, as well as how to connect databases such as Oracle and mySQL using DBI. SQL will also be introduced in the tutorial.

This is a hands-on workshop. Attendees will have the opportunity to create a simple web database during the workshop.

NWChem is a program that can be used to calculate a variety of chemical properties. NWChem is primarily used for carrying out electronic structure calculations. This tutorial will give an overview of the program capabilities, a detailed description of how to run the program here at the Institute, and tips on how to run jobs efficiently.

Molecular modeling is a general term that covers a wide range of molecular graphics and computational chemistry techniques that are used to build, display, manipulate, simulate and calculate molecular properties. InsightII is a graphic user interface that acts as a front end to many of these molecular modeling tools. This workshop covers the basic biomolecular building and visualization features within InsightII, in addition to demonstrating its interface to some of its molecular modeling modules.

From the Web to PowerPoint presentations, animations and graphics are powerful collaboration and research tools. This tutorial will introduce some powerful tools for generating high-quality molecular images and animations for both the biologist and the chemist. We will focus on using Amira and PyMol for producing and manipulating molecular pictures and various tools for generating animations from the created images.

In the technical computing environment, MATLAB is a powerful high-level programming language. This tutorial will help researchers solve some computational problems using MATLAB functions without spending much time dealing with programming details. We will start with a quick review of MATLAB’s syntax and I/O handlers. More attention will be focused on the use of some computational functions and toolboxes.

Users are encouraged to contact the User Support Staff (help@msi.umn.edu or (612) 626-0802) about the computation problems you need to solve and/or some specific issues that you meet in solving them. We will use this information to make the tutorial more productive.

This tutorial consists of two parts:

1. A 50-minute lecture describing the MATLAB functions

2. An optional one-hour, hands-on session focusing on the use of these functions for your application.

GAMESS is a program that can be used to calculate a variety of chemical properties. GAMESS is primarily used for carrying out electronic structure calculations. This tutorial includes an overview of the program capabilities, a detailed description of how to run the program here at the Institute, and tips on how to run jobs efficiently.